...August 2013We now have information about ~550 resources!. Visual navigation added May 2010Click the 'Database interactions' link on the left menu to access. Major updateAll resources were recently reviewed and many new ones were added Get the StatsDetailed Pathguide resource statistics now available Pathguide PublishedPlease cite the Pathguide PublicationProtein-Protein Interactions Database Name (Order: alphabetically | by web popularity alphabetically | by web popularity ) Full RecordAvailabilityStandards2P2Idb - The...

...August 2013We now have information about ~550 resources!. Visual navigation added May 2010Click the 'Database interactions' link on the left menu to access. Major updateAll resources were recently reviewed and many new ones were added Get the StatsDetailed Pathguide resource statistics now available Pathguide PublishedPlease cite the Pathguide PublicationProtein-Protein Interactions Database Name (Order: alphabetically | by web popularity alphabetically | by web popularity ) Full RecordAvailabilityStandards2P2Idb - The...

...ServerThis is the web server BIPS (Biana Interolog Prediction Server). Here, you can predict putative interactions between proteins based on homologs found in Protein-Protein interaction databases. BIPS relies on data integrated in BIANA. You just need to insert your sequences of interest or list of protein identifiers, and BIPS will infer interactions based on homology. Predicted partners can be restricted to proteins added in your list or to the complete BIANA database. If you are unsure on...

...et al. 2015Received: 14 February 2015Accepted: 22 May 2015Published: 6 June 2015AbstractBackgroundDuring spliceosome assembly, protein-protein interactions (PPI) are sequentially formed and disrupted to accommodate the spatial requirements of pre-mRNA substrate recognition and catalysis. Splicing activators and repressors, such as SR proteins and hnRNPs, modulate spliceosome assembly and regulate alternative splicing. However, it remains unclear how they differentially interact with the core spliceosome to perform their functions.ResultsHere, we investigate the protein connectivity of...

...for many pathogens. However, many questions are relatively unexplored. What are the properties of human proteins that interact with pathogens? Do pathogens interact with certain functional classes of human proteins? Which infection mechanisms and pathways are commonly triggered by multiple pathogens? In this paper, we provide the first study of the landscape of human proteins interacting with pathogens. We integrate human-pathogen protein-protein interactions (PPIs) for 190 pathogen strains from seven public databases. Nearly all of the 10,477...

...http://caps.ncbs.res.in/peptidemine/ text/html; charset=utf-8 PeptideMine | Peptide Substrates from Interacting Proteins Home ServerSearch & SubmitHelpGroupPeptideMine - WebServer for Identification and analysis of peptides from interacting proteins : PeptideMine is a webserver developed for identifying and analysing peptides suitable for protein-peptide binding studies. PeptideMine is using a unique, knowledge based approach for the identification of peptides from the interacting sequence-space of a protein using different search programs (PeptideMine Search, BLASTP and regular expression...

25348397 http://comppi.linkgroup.hu/ text/html; charset=us-ascii ComPPI - Main PageCompartmentalized Protein-Protein Interaction DatabaseHomeSearchDownloadsHelpTutorialContact UsWhat is ComPPI?Protein-protein interaction networks are spatially and temporally merged from the results of various experimental and predicting methods. These often ignore localization data, which in turn deteriorates the data quality and its predictive potential.We present ComPPI, the compartmentalized protein-protein interaction database, which provides qualitative information on the interactions, proteins and their localizations integrated from multiple...

21036873 http://www.megabionet.org/atpid/webfile/ text/html; charset=utf-8 AtPID AtPIDArabidopsis thaliana Protein Interactome DatabaseQUICK START:Please enter a single protein when you would like to know if some other protein can interact with it. Otherwise, enter a pair of protein to check if they can interact with each other according to our data collections and predictions. AtPID can identify a variety...

...bclab.inha.ac.kr/pridictor/ text/html; charset=utf-8 PRIdictorï»¿ As many structures of protein-RNA complexes have been known in the past years, several computational methods have been developed...the past years, several computational methods have been developed to predict RNA-binding sites in protein. However, its inverse problem (i.e., predicting protein-binding sites in RNA) has received much less attention. Furthermore, most of the methods that predict RNA-binding sites in protein do not consider interaction partners (i.e., RNAs) of a protein, so they always predict the same binding sites for a given protein sequence even if...

...text/html; charset=utf-8 About - iRefWeb - Wodak LabAbout - iRefWeb - Wodak LabYou have:discovered a protein or a gene likely to be involved in a disease, and you want to find out what is known about its interactions with other proteins.identified a group of co-expressed genes, and would like to check if the proteins they code for interact physically.found a set of genes associated with a specific phenotype, or a cellular process...

...text/html; charset=us-ascii UsageOverview Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program called ModuleSearch...

...html; charset=us-ascii Probabilistic Local WalksProbabilistic Local WalksAn Accurate And Efficient Method For Detecting Protein Complexes from Protein-Protein Interaction NetworksDownload this project as a .zip file Download this project as a tar.gz fileWhat is PLW?PLW (Probabilistic Local Walks) is a graph clustering algorithm, and was designed to detect protein complexes in protein-protein interaction (PPI) networks with high accuracy and efficiency.PLW uses a seed selection strategy to prioritise...

...phase transitions that drive ribonucleoprotein granule assembly. In this paper, we report many PLDs in proteins associated with paraspeckles, subnuclear bodies that form around long noncoding RNA. We mapped the interactome network of paraspeckle proteins, finding enrichment of PLDs. We show that one protein, RBM14, connects key paraspeckle subcomplexes via interactions mediated by its PLD. We further show that the RBM14 PLD, as well as the...

...text/html; charset=us-ascii Apoptosis database HomeResearchMembersCoursesGrants and AwardsJobs and OpeningsExtending signalling pathways with protein-interaction networks. Application to apoptosis.Extending signalling pathways with protein-interaction networks. Application to apoptosis. Joan Planas-Iglesias, Emre Guney, Javier Garcia-Garcia, Kevin A. Robertson...present the supplementary materials and complete numerical results for the paper "Extending signalling pathways with protein-interaction networks. Application to apoptosis.". In this work, we build four different apoptotsis-related networks from the 53 hand-curated apoptotsis-related proteins known by 20051 (referred as seeds). These seeds are connected in networks according to the...

...and Drugs Online ResourcePlease enter your search below, or browse the list of drugs or proteins.About MATADORMATADOR is a resource for protein-chemical interactions. It differs from other resources such as DrugBank in its inclusion of as many direct and indirect interactions as we could find. In contrast, DrugBank usually contains only the main mode of interacton...

...usOverviewMembersFacilitiesGT Login (CSSB staff)Skolnick Research GroupPublicationsNews & EventsNewsDistinguished Lecture SeriesUpcoming SeminarsPast SeminarsSoftware & ServicesServicesSoftwareDatabasesSimulationsJobs APoc Most proteins interact with small-molecule ligands such as metabolites or drug compounds. Over the past several decades, many of these interactions have been captured in high-resolution atomic structures. From a geometric point of view, most interaction sites for grasping these small-molecule ligands, as revealed in these structures, form concave shapes...

27208273 http://netbio.sjtu.edu.cn/arappinet/ text/html; charset=us-ascii Welcome to AraPPINetAraPPINet - Protein-Protein Interaction Network for Arabidopsis The global Arabidopsis PPI network (AraPPINet) that was inferred from both three-dimensional structures and functional evidence and that encompasses 316,747 high-confidence interactions among 12,574 proteins(download arappinet full dataset). AraPPINet exhibited high predictive power for discovering protein interactions at a 50% true positive rate and for discriminating positive interactions from similar protein pairs...

...narrow down their dataset. Once a term is selected, you are taken back to the interaction tab to review your dataset.Bulk linking to third party resources by using involved proteinsProteins by Reactome pathway: Sends your proteins to the Reactome SkyPainter that will show you the pathways in which these molecules are know to play a role. Proteins by Chromosomal location: Sends your list of proteins to Ensemblâs Karyotype viewer and...

...UbiNet UbiNet is a knowledge-based system thatÂ could provide potential E3 ligases for ubiquitinated proteins by the information of protein-protein interactions and substrate site specificities. In eukaryotes, protein ubiquitination catalyzed by E3 ubiquitin ligases plays crucial roles in regulating a variety of biological...there exists no resource designed to explore the regulatory networks of E3 ligases for ubiquitinated proteins in humans. Therefore, the UbiNet was designed to provide a full investigation of protein ubiquitination networks by integrating all available ubiquitinome datasets, experimentally verified E3 ligases, and protein-protein interactions. Moreover, UbiNet could provide potential E3 ligases for ubiquitinated proteins by the information of protein...

...ANCHOR?ANCHOR is a web-based tool whose aim is to facilitate the analysis of protein-protein interfaces with regard to its suitability for small molecule drug design.ANCHOR visualization toolThe idea behind itSmall molecule inhibitors of protein-protein interactions often bind to the hotspot areas at the protein-protein interface. The identification of hotspots residues thus constitute valuable information to be exploited on the...